All Published Workflows

5 workflows that have been reviewed and published

nanopype
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Snakemake pipelines for nanopore sequencing data archiving and processing
public

public

Detailed documentation and tutorials are available at readthedocs . Nanopype is a snakemake based pipeline providing conv...
Sample annotation Base-calling Alignment sniffles svim bedGraphToBigWig BEDTools Flye GUPPY Minimap2 nanopolish NGMLR Pandas Racon SAMtools Singularity Hub Snakemake wtdbg2 graphmap2 matplotlib numpy oschmod seaborn nanopore
Free
87
genome_tracks
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A Snakemake workflow for easy visualization of genome browser tracks of aligned BAM files powered by the wrapper gtracks for the package pyGenomeTracks.
public

public

A Snakemake workflow for easy visualization of genome browser tracks of aligned BAM files (e.g., RNA-seq, ATAC-seq,...) p...
Sample annotation Trajectory visualization Alignment DeepTools SAMtools Snakemake RNA-Seq
Free
7
mtoolbox_snakemake
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MToolBox pipeline written in snakemake to allow a better scalability
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public

This is an work-in-progress update of MToolBox ( PMID:25028726 ). Please find more at the official documentation .
VCF raw sequence reads Genetic mapping Alignment gatk BCFtools FastQC Picard SAMtools Snakemake Trimmomatic Genomics
Free
22
snakemake-umetaflow
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Created for testing the metabolomics pipeline through snakemake
public

public

This is the Snakemake implementation of the pyOpenMS workflow tailored by Eftychia Eva Kontou and Axel Walter ...
Gene ID Nextflow Quantification Alignment Nextflow Pandas Pyteomics Snakemake networkx numpy Gene structure
Free
6
detectmutations
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singularity & snakemake workflow to detect mutations with several tools to detect mutations
public

public

Sylvain Schmitt April 20, 2021 Installation Usage Get data Locally HPC Work...
raw sequence reads Sequence mutation and randomisation Alignment gatk BEDTools Biostrings BWA FastQC FreeBayes MultiQC QualiMap SAMtools Snakemake Trimmomatic vcfR tidyverse Quality affairs
Free
29